Mitochondrial gene diversity was used in house fly, Musca domestica L., populations to examine gene flow within and among 16 sealed barns in a large egg-laying facility in Renville, MN. Haplotypes in poultry barns were compared with those in outdoor house fly populations nearby and in St. Paul, MN. Haplotype diversities were greater in the closed than in the open populations. There was significant gene flow among poultry barns, and export of flies from barns was observed. Nevertheless, of three haplotypes detected in the closed populations, one was undetected in the open populations. A significant change in haplotype frequencies within poultry barns between years is attributed to genetic drift. The geographical origin of one haplotype is obscure.